NAME (printed)
SIGNATURE SS#
BIOL 303 - CELL BIOLOGY
EXAM1
TUESDAY, OCTOBER 2,200l
GENERAL INSTRUCTIONS
1.
WRITE YOUR NAME ON EACH PAGE. USE PEN, NOT PENCIL.
2.
WRITE LEGIBLY!! PEOPLE LOSE POINTS BECAUSE WE CAN’T
READ THEIR ANSWERS.
3.
PACE YOURSELF - DO NOT GET STUCK ON ANY ONE
QUESTION.
4.
NOTE THE POINT VALUE OF EVERY QUESTION. THERE ARE
70
POINTS.
5.
WHEN EXPERIMENTAL EVIDENCE IS CALLED FOR PROVIDE
PROCEDURES, RESULTS AND CONCLUSIONS UNLESS
OTHERWISE NOTED IN THE QUESTION.
6.
KEEP YOUR ANSWERS BRIEF. DO NOT RAMBLE. IT IS A
WASTE OF TIME AND IT OFTEN INDICATES YOU DON’T KNOW
THE CORRECT ANSWER.
IT MAY RESULT IN POINT
DEDUCTIONS.
7.
THEREARE 3
8.
2
QUESTIONS ON THIS EXAM.
PLEASE NOTE. YOU NEED NOT USE ALL THE SPACE PROVIDED
FOR EACH QUESTION.
Part1 - Blumberg questions - 40 points.
1) (3 points) Name 3 structures present in eukaryotic cells that are not in prokaryotic cells.
2) (2 points) What is the difference between a lytic virus infection and a lysogenic virus infection ?
3) (3 points) What are the 3 components of the “ Cell Theory” ?
4) (3points) List 6 functions of the plasma membrane.
5) (2 points) What method can separate cellular components on the basis of density ?
6) (2 points) Why does electron microscopy give much higher resolution than light microscopy ?
7)( 1 point) Which of the following will improve resolution of objects under the microscope ?
a. decreasing the retiactive index of the medium that the sample is in
b. decreasing the wave length of light illuminating the sample
c. decreasing the numerical aperture of the objective
d. increasing the magniijcation of the objective
e. staining the sample
8) (1 point) Under which conditions would the visibility of an object under a microscope be
lowest ?
a. The object has the same refractive index as the medium
b. The object and the background each bend light differently
c. The object difEacts some but not all of the light rays that hit it
d. The object absorbs some but not all of the light rays that hit it
e. The sample is stained with eosin
9) (2 points) A membrane’s transition temperature is determined and found to stretch over a wide range of
temperatures. The membrane also exhibits high stability and a reduced permeability similar to that in
most mammals. What membrane component is responsible for these traits and how does it do it?
10) (3 points) A rat cell and a chimpanzee cell are f&d together. Antibodies to chimpanzee membrane
antigens are labeled with rhodamine (a red fluorescent molecule) and antibodies against rat antigens are
labeled with fluorescein (a green fluorescent molecule). What do the cells look like immediately after
fusion? What about 40 minutes later? If the temperature of the cell is increased, what should happen?
11) ( 2 points) You carry out an experiment using the FRAP technique to determine the relative speed of
diffusion of two proteins, A and B. Protein A has a molecular weight of 175,000 daltons and B a
molecular weight of 35,000 daltons. Which protein results in the faster fluorescence recovery time?
12) (2 points) What would happen if a FRAP assay were carried out on a 35,000 dalton protein whose
movement is restricted?
13) (2points) Assume that a red blood cell with an internal osmolarity equivalent to 0.15 M NaCl is
placed in a solution with a concentration of 0.35 M NaCI.
a. What happens to the cell?
b. What word descriis the interior of the cell relative to the solution surrounding it?
c. What word descriis the solution surrounding the red blood cell relative to its internal
concentration?
d. If the solution surrounding the cell also had a concentration of 0.15 M NaCI, what word would
describe it?
14) (1 point) Cholesterol mixes with phosphoiipids in a biomembrane because cholesterol molecules
are
a. amphipathic
b. steroid derivatives
c. entirely hydrophobic
d. phospholipid derivatives
15) (1 pomt) The two leaflets of a biomembrane can be separated and visualized by
a. differential interference contrast microscopy
b. photobleaching
c. low angle X-ray scattering
d. keze fkacture, freeze etch electron microscope
.
16) (2 points) How do carbohydrates associate with biomembranes?
17) (I point) Peripheral membrane proteins
a. contain membrane spanning domains
b. interact with the phospholipid core of the phospholipid bilayer
c. can be bound to the membrane indirectly by interactions with the lipid polar head
d. contain many amino acids with hydrophobic residues
18) (I point) Membrane proteins can be anchored to the plasma membrane by all of the following
except
a. a hydrocarbon moiety such as farnesyl
b. a fatty acyl group such as palmitate
c. a glycosylated phospholipid such as glycosylphophatidylinositol
d. a simple sugar such as mannose
19) (6 points) Membrane proteins were extracted with SDS and subjected to SDS-polyacrylamide
gel electrophoresis on tube gels. The resultant gels were stained with Coomassie Blue, which
stains proteins (a), and Periodic Acid-Schiff (PAS) stain, which specifically stains carbohydrates
(b).
When whole cells or inside-out vesicles were exposed to lactoperoxidase and ‘=I, the profile in
Graph (c) was obtained when the gels were cut into 1 mm thick slices and the radioactivity was
monitored in the scintillation counter. In Graph (d), we see the results of exposure to galactose
oxidase and %I - borohydride, a process that radioactively labels sugar residues to which
galactose oxidase and %I - borohydride are exposed. In Graphs (c) and (d), the Black line
indicates labeling of whole cells and the GREY lines indicate labeling of inside-out vesicles.
What kind of membrane proteins are A, B, C and D? (That is., on which surface are they
exposed? Do they have polysaccharides attached and on which side of the membrane are the
polysaccharides exposed, if present?) Ignore any preconceived notions about membrane
proteins! Just interpret the data!!!
(4
(b)
OD
OD
Distance 13~~e&+n.ing
Distance ~-oe~eginning
Distance ~~n-&3eginning
Distance Fr;re3eginning
(c)
CPM
1251
Exposure on intracellular or
extracellular surface?
Is it a glycoprotein?
Which leaflet has the sugar
group (if any)?
c 1. (1 pt) A, when a carbohydrate is fully metabolized to produce ATP, what happens to its carbon atoms?
B. What is the chemical role of oxygen in this process?
C2. (1 pt) From the viewpoint of a muscle cell,
A. What is an important advantage of glycolysis?
B.
What is the major disadvantage
or limitation of glycolysis?
C3. (2 pts) A. What are the 2 (two) soluble coenzymes/electron carriers in mitochondria that 1in.k glycolysis
and the Krebs (TCA) Cycle with Electron Transport?
B. How do they function?(in the most general way)
C. Are they also used in chloroplasts? (Explain)
Cd. (2 pts) A. What is the general name (not how it works) of the hypothesis that explains how electron
transport is coupled with ATP synthesis? (Also, not the name of the scientist who devised it.)
B. What 2 (two) things does this hypothesis predict or require about the appropriate mitochondria membrane?
(Expts or explanations of how it works are not wanted.)
C5. (3 pts)What is 1 (one) experiment that directly supports this hypthesis (of Q #C4)? Give the experimental
system, the relevant observations, and the important interpretations/explanation relevant to the hypothesis.
C6. (2 pts) A. What is the full name of the “force” that drives ATP production in mitochondria, and of what
chemical/physical parameter(s) is it composed? (Given names, not abbreviations)
B. In what way is it different/modified in chloropIasts (compared to mitochondria) ?
CT. (1 pt) What is the significance (“reason”) for the ‘Z-scheme” in the mechanism of the light reaction in
chloroplasts?
C8 (4 pts) Compare and contrast the light and dark reactions in chloroplasts in terms of:
Light Rxn
Dark Rxn
A. What happens in each (the results
of each rxn)(very general)
3. structural location?
C. Whether ATP is produced
or used:
0. (2 pts) What is/are ‘bistae” in terms of:
A. their structure (words and diagram are OK), and where they are found in plants cells:
B. their major function(s) (i.e.. what happens in them?)
C lo. (2 pts) A. In “happy” mitochondria, what would the maximum P/O ratio be when the electrons entered the
ET. Chain at its “first”/most upstream” point?
B. Why?
Cl 1. (3 pts) In “happy”, well coupled mitochondria, what would happen to the 02 (oxygen) consumption and to
ATP synthesis after different experimental conditions were established (in the following different expts). Your
choices are: increases, stays same, decreases/stops
02 consumrdion
Expt#l: An inhibitor of oxid.
phosphorylation added.
(e.g., oligomycin)
ExpbY2: same as Expt#l , but
an uncoupler also added.
(e.g. DNP)
Fsptff3: only an uncoupled
‘1 added
C 12. (1 pt) In non-cyclic photophosphotylation,
A. What is the ultimate source of the electrons?
B. What ultimately “drives” the reaction?
ATP synthesis
Cl3 (6 pts) Given 5 electron carriers in a martian mitochondria (very similar to human mito’s) A B C D E (in
this order):
A. Where would you expect oxygen to act? (These mito use 02)
B. Which carrier would have the most negative standard redox potential (weakest electron acceptor) ?
C. What is 1 (one) experimental way you could use to determine the order of all carriers in this ET. patQway?
(Describe the experimental system and what the observations would be.)
NAME (printed)
SIGNATURE
SS#
BIOL 303 - CELL BIOLOGY
EXAM III
Friday, December 14, 2001
GENERAL INSTRUCTIONS
1.
WRITE YOUR NAME ON EACH PAGE. USE PEN, NOT PENCIL.
2.
WRITE LEGIBLY!! PEOPLE LOSE POINTS BECAUSE WE CAN’T
READ THEIR ANSWERS.
3.
PACE YOURSELF - DO NOT GET STUCK ON ANY ONE
QUESTION.
4.
NOTE THE POINT VALUE OF EVERY QUESTION. THERE ARE
100 POINTS.
5.
WHEN EXPERIMENTAL EVIDENCE IS CALLED FOR PROVIDE
PROCEDURES, RESULTS AND CONCLUSIONS UNLESS
OTHERWISE NOTED IN THE QUESTION.
6.
KEEP YOUR ANSWERS BRIEF. DO NOT RAMBLE. IT IS A
WASTE OF TIME AND IT OFTEN INDICATES YOU DON’T KNOW
IT MAY RESULT IN POINT
THE CORRECT ANSWER.
DEDUCTIONS.
7.
THERE ARE 37
8.
PLEASE NOTE: YOU NEED NOT USE ALL THE SPACE PROVIDED
FOR EACH QUESTION.
QUESTIONS ON THIS EXAM.
I)(2 points) Name 4 different ways that a substance can move across the plasma membrane.
2)(2 points) Describe 2 ways in which the energy to move ions or solutes against a concentration
gradient can be generated.
3) (2 points) The energy required for the transport of K’ out of the cell is the sum of what ?
4) (2 points) What is the partition coeffkient and what is its relation to membrane permeability
of a solute ?
5)(3 points) What properties distinguish a transporter protein Corn a channel protein and which
has the faster rate of transport and why ?
6) (2 point) What is the role of GTP in the assembly of microtubules and how does it influence
i
dynamic instability ?
7) (5 points) Name 2 microtubule motor proteins and for each indicate what kind of transport
they carry-out and describe the structure of the proteins and what role each major part of the
protein has.
The microtubule motor proteins are a large family of proteins. With in the protein families, what
part of the protein would you expect to be most highly diverged and why ?
What part would you expect to be most conserved and why ?
8) (5 points) Where are microtubules assembled and what is the role of gamma tubulin in the
assembly process. ? Describe microtubule polarity and how gamma tubulin helps to establish
polarity. Which end of the microtubule extends to the edges of the cell ?
9) (1 point) What structure serves as the organizing center for flagella ?
IO) (2 points) Name a key difference between in the composition of intermediate filaments and
the other 2 cytoskeletal components, the microtubules and the microfilaments.
How does the assembly of intermediate filaments differ from the assembly of both microtubules
and microfilaments ?
11) (2 points) HOW was the polarity of microfilaments determined and how is the + end defined’?
12) (1 poin&WJat is meant by treadmilling ?
13) (2 points) Give 2 examples of motility that depends on Actin polymerization alone (myosin is
not involved).
14) (3 points) The distance that the myosin motor moves an actin microfilament depends upon
what part of the myosin motor protein and how was this determined ?
15) (2 points) The gene for conventional or type II myosin was inactivated in Dictyostelium cells
resulting in what surprising result and what did this tell us about the role of myosins I and II in
the cell ?
16) (2 points) What is the major difference in structure between Type II (conventional myosin)
and Type I (unconventional myosin) (you may make a drawing of each).
17) (2 points) If you compared under the microscope a contracted sarcomere to a relaxed
sarcomere which of the following regions would not differ in width ?
A) the A band
B) the I band
C) the H zone
D) the entire sarcomere
18) (2 points) What is the role of Titan and of Nebulin in the muscle sarcomere ?
19) (5 points) What is the role of Ca++ in muscle contraction and describe how Ca ++ levels are
regulated in muscle cells during excitation/contraction coupling from the time when a nerve
impulse is sensed at the neuromuscular junction to the point where the muscle relaxes again.
(3 points) Name 3 different classes of actin binding proteins and describe their function
Mefly)
20)
21) (3 points) In order for a cell to extend a pseudopod or a lamellipod, binding of a ligand to a
cell surface receptor initiates the formation of an actin network at the cell cortex which will push
the cortex outward. Nucleation of the actin network requires what complex of actin binding
proteins ?
Where are these protein located in the network that forms and how do we know this ?
22) (6 points) During mitosis there are 3 types of microtubules that form the mitotic spindle.
What are they and what is their function during mitosis ?
23) (2 points) During Mitosis there is a check point where the cell checks to determine that the
chromosomes are correctly aligned on the metaphase plate. What 2 things must happen for the
cell to progress through theis check point ?
24) ( 3 points) What determines the plane of cleavage during cytokinesis ? Briefly describe an
experiment that demonstrates this.
25) (6 points) Three types of proteins regulate the activity of G proteins. What are these proteins
and how do they work ?
26) (1 points) In paracrine signaling, the signaling molecule
a. acts on target cells far away from the secreting cell
b. acts on target cells in close proximity to the secreting cell
c. acts on the same cell that secretes the signaling molecule
d. is carried to the target cell by the blood
27) (5 points) What are 2 different effector molecules activated by G protein coupled receptor
systems and what are the second messengers that are generated by activation of these effecters ?
28) (1 point) Binding of hormone to a receptor tyrosine kinase causes all of the following except
a. dimerization of the receptor
b. autophosphorylation of the receptor
c. activation of Ras through an interaction with GRB2 and SOS proteins
d. hydrolysis of GTP bound to Ras
29) (1 point) All of the following steps are part of the kinase cascade that transmits signals down
Corn activated Ras protein except
a. ras phosphorylates Raf
b. rafphosphorylates MIX
c. MEK phosphoxylates MAP lcinase
d. MAP kinase phosphorylates target proteins
30) (3 points) Describe the role of the SH2 adapter proteins in the activation of Ras by receptor
tyrosine kinases.
3 1) (4 points) To what kind of ligands do integrin receptors bind ? Name 2 different pathways
that can be activated by integrin receptor binding to its ligand. Integrin receptors are found
associated with what structures ?
32) (4 points) Programmed cell death results in the activation of enzymes known as
Theses enzymes execute the cell death program by degrading what cellular targets ? (describe 3
of their targets).
33) (1 point) The intracellular cascade for programmed cell death requires the binding of the
bcl2 family member Bad to a receptor on what cellular organelle ?
a. chloroplast
b. mitochondrion
c. nucleus
d. Zellweger’s body
Cl. (1 pt) What is the implication or significance of the “premature chromosome condensation” observation
relevant to the mammalian cell cycle?
C2. (1 pt) How can you experimentally distinguish a cell in G2 from a cell in Gl?
C3. (4 pts) What are at least 4 important properties/characteristics of “cyclin”? (Including its biochemical
composition, function[s], intracellular concentration, and what controls its activity)
C4. (4 pts) A. what is the full name of “MPF” (involved in the cell cycle) ?
B. What does it do biochemically when active?
C. Briefly explain how kinases and phosphatases regulate its activity. (Ignore the role of other things that also
can affect its activity.)
NAME (printed)
SIGNATURE
SS#
BIOL 303 - CELL BIOLOGY
EXAMII
Tuesday, November 6, 2001
GENERAL INSTRUCTIONS
1.
WRITE YOUR NAME ON EACH PAGE. USE PEN, NOT PENCIL.
2.
WRITE LEGIBLY!! PEOPLE LOSE POINTS BECAUSE WE CAN'T
READ THEIR ANSWERS.
3.
PACE YOURSELF - DO NOT GET STUCK ON ANY ONE
QUESTION.
4.
NOTE THE POINT VALUE OF EVERY QUESTION. THERE ARE
90 POINTS.
5.
WHEN EXPERIMENTAL EVIDENCE IS CALLED FOR PROVIDE
PROCEDURES, RESULTS AND CONCLUSIONS UNLESS
OTHERWISE NOTED IN THE QUESTION.
6.
KEEP YOUR ANSWERS BRIEF. DO NOT RAMBLE. IT IS A
WASTE OF TIME AND IT OFTEN INDICATES YOU DON’T KNOW
THE CORRECT ANSWER.
IT MAY RESULT IN POINT
DEDUCTIONS.
7.
THERE ARE 33
8.
QUESTIONS ON THIS EXAM.
PLEASE NOTE: YOU NEED NOT USE ALL THE SPACE PROVIDED
FOR EACH QUESTION.
1. ( 1 pt) In eukaryotic chromosomes, DNA is complexed with histones to form
2. (2 pts) Clearly distinguish between the concepts of “chromosome” and “chromatin” as defined in
chs:
3. (3 pts) What are 3 ways in which a bacterial “chromosome” is different from an human “chromosome”?
4. (4 pts) What is the composition and structure of a core nucieosome? (Either description or a fully IabelIed
diagram)
5. (1 pt) What connects adjoining nucleosomes ?
6. (3 pts) What is the experimental evidence that there may be a “scaffold” for eukaryotic chromosomes?
7. (1 pt) Of what type(s) of macromolecule(s) is the chromosome s&old likely to be composed?
8. (3 pts) What is the “proteasome” and what is its function in an eukaryotic cell?
9. (2 pts) What is “autophagy” and what is its function in an eukaryotic cell?
10. (5 pts) A.What is “receptor mediated endocytosis”(REM) ?
B. What is/are the name(s) of the initial structure(s) involved in REM?
C. What are at least 3 different different types of proteins are associated with this/these structure(s)?
11. (3 pts) How can you distinguish between rough endoplasmic reticulum (rER) and smooth endoplasmic
reticulum (sER):
a. structurally (be precise - not “roux vs “smooth”)
b. functionally
form.
12. (1 pt) The proteins transported into the ER are in their
13. (4 pts) A. What is the difference between cotranslationaiand post-translational movement of proteins?
B. How can they be experimentally distinguished?
14. (2 pts) A. How are chaperone proteins involved in the movement of various proteins into various cell
compartments?
B. Does their functioning require “energy” (Yes
or
No)
15. (4 pts) A. What is/are the role(s) of nuclear lamina?
B. of what general type(s) of macromolecule(s) is it composed?
C. What is its structure during the cell cycle?
D. What regulates its structure/function?
16. (4 pts) A.What are
the 2 (two) different ways in which different molecules can enter or leave the
nucleus?
B. What parameter(s) play an important role in determining which mechanism is used for a given
molecule and if a given molecule even enters?
17. (2 pts) What determines the “unidirectionality” of the movement of specific macromolecules into or out of
the nucleus and why? (Be reasonably complete in your answer)
18. (3 pts) What is the experimental evidence that eukaryotic chromosomes have multiple replicoos?
19. (2 pts) What is the significance for eukaryotic cells of multiple replicons?
20. (4 pts) A. What is the phenomenon of “editing”?
b. How is it experimentally shown to exist?
C Hnw common is it?
(And give 1 example)
2 1. (2 pts) What is meant by the statement “not all mitochondria follow the universal genetic code”?
22. (4 pts) What are some of the very unusual features observed in human mitochondria in terms of its genome
structure and process(es) by which it makes each of its mRNA’s? (Need at least 4 for 111 credit)
23. (4 pts) Draw a rough diagram of the Golgi, and label all important parts, and make clear how its
orientation can be recognized:
24. (3 pts) What are 3 important l?.mctions of Golgi?
25. (2 pts) How does most material move through the Golgi on a short time scale ?
26. (2 pts) How ddes the Golgi keep its important enzymes from “escaping” or being secreted?
27. (1 pt) Plasma membrane proteins are first inserted into the membrane in the
(Which structure/organelle)
28. (3 pts) A. Where are the phospholipids of all eukaryotic cell membranes synthesized? (Be very precise)
B.From their site of synthesis, how are the newly made phospholipids fully distributed to all of the
cell’s bilayer membranes? (For full credit, need at least 2 mechanisms)
29. (4 pts) In the initial glycosylation of eukaryotic proteins:
A. what organelle(s) is/are involved?
B. what is the role of dolicol ?
C. what determines which sugars are added?
D. are nucleotide triphosphates other than ATP involved? (Yes or No)
30. (2 pts) If you isolated mR.NA that was part of the ER, and characterized what proteins it coded for A Whslt cs nf different cellular compartment membrane proteins would they include? (need at least .3)
b. Which (if any) cell compartment membrane proteins would they NOT code for?
3 1. (4 pts) A. Why is the regular DNA replication system (with DNA-dependent DNA polymerases, primae,
ligase, etc) adequate and sufficient for bacteria, but not for eukaryotic cells?
B. So what do eukaryotic cells have in addition for their complete chromosome DNA replication system?
32. (1 pt) The address information (“zip code”) for protein sorting in a eukaryotic cell is contained in the
of the proteins.
33. (4 pts) A. What is the role of “SNARES” in the trafficking of proteins thru the cell?
B. And how do they function ?